The ability to identify proteins and determine their chemical structures has become central to the life sciences. The amino acid sequence of proteins provides a link between proteins and their coding genes via the genetic code, and, in principle, a link between cell physiology and genetics. The identification of proteins provides a window into complex cellular regulatory networks.
Ion trap mass spectrometers are among the most widely used platforms for molecular analysis—spanning natural products, to pharmaceuticals, to biologics such as proteins. Most mass spectrometer-based experiments begin with the isolation of a group of compounds from a set of samples through some sort of extraction technique, e.g., proteins from tissues, cell lysates, or fluids followed by proteolytic digestion of those proteins into peptides (i.e., bottom-up proteomics). Frequently, but not necessarily, the mass spectrometers are then coupled with some form of separations, e.g., electrophoretic or chromatographic. Over the course of just a few hours, mass spectral instruments can autonomously interrogate tens of thousands of molecular species via tandem mass spectrometry.
Although some of the initial descriptions of low-energy collision activated dissociation tandem mass spectrometric analysis were performed using beam-type dissociation on triple quadrupole mass spectrometers, due to the speed and sensitivity of quadrupolar ion trap analyzers, resonant-excitation collision activated dissociation is arguably the most widely used dissociation method for many common types of analyses (e.g., bottom-up proteomics, glycomics, etc.). Recently though, there has been a surge in interest in beam-type collision activated dissociation—particularly its application towards the interrogation of precursors that are typically not amenable to resonant excitation collision activated dissociation (e.g., phosphorylated peptides, metabolites, etc.).
Developed in parallel with these rising interests, hybrid instruments that possess multiple analyzers and multiple means of peptide fragmentation—including beam-type collision activated dissociation—have become common place (e.g., the LTQ-Orbitrap, and the Velos-Orbitrap). One common element to all of these instruments that are capable of beam-type collision activated dissociation is that they have dedicated collision cells for conducting the fragmentation technique. The price for enabling beam-type collision activated dissociation on these instruments, therefore, is increasing instrument complexity and cost.
The characteristics and performance of commonly used types of mass spectrometers are presented in Table B1. Check marks indicate available, check marks in parentheses indicate optional. Pluses indicate possible or moderate (+), good or high (++), and excellent or very high (+++), respectively. Seq., sequential.
TABLE B1Characteristics and Performance of CommonlyUsed Types of Mass Spectrometers*Q-Q-ToF-IT-LIT1ToF2ToF3FT-ICR4Q-Q-Q5QQ-LIT6Mass accuracyLowGoodGoodExcellentMediumMediumResolvingLowGoodHighVery highLowLowpowerSensitivityGoodHighMediumHighHigh(LOD)Dynamic rangeLowMediumMediumMediumHighHighESI7✓✓✓✓✓MALDI8(✓)(✓)✓MS/MS✓✓✓✓✓✓capabilitiesAdditionalSeq.Precursor,Precursor,Precursor,capabilitiesMS/MSNeutralNeutralNeutralloss, MRMloss, MRMloss, MRM9Identification+++++++++++Quantification++++++++++++++Throughput++++++++++++++Detection of+++++++modifications*Table adapted from Domon and Aebersold, Science 14 Apr. 2006: Vol. 312. no. 5771, pp. 212-2171Ion Trap - Linear Ion Trap,2Quadruple-Quadruple - Time of Flight,3Time of Flight - Time of Flight,4Fourier Transform - Ion Cyclotron Resonance,5Quadruple - Quadruple - Quadruple,6Quadruple - Quadruple - Linear Ion Trap,7Electrospray Ionization,8Matrix Assisted Laser Desorption/Ionization,9Multiple Reaction Monitoring
As can be seen from Table B1, a multitude of different mass-spectral techniques and instrumentation have been developed over the years. Many mass-spectral instruments have been designed to carry out one type of mass-spectral analysis without the ability to carry out other types or are very limited in their scope of application. This has led to instruments of increasing complexity designed to carry out increasingly complex mass-spectral analysis. The increasing complexity of instruments designed to carry out MSn analysis, for example, has led to increasing costs for such instruments. These instruments add a separate mass selection region for each additional MS step, which increases the cost and complexity with each added MS step capability. A need, therefore, exists in the art for the ability to perform MSn experiments without the need to increase the complexity and cost of traditional MS or MS/MS instruments.